Main_Random Forest

if(!require("EBImage")){
  install.packages("BiocManager")
  BiocManager::install("EBImage")
}
if(!require("R.matlab")){
  install.packages("R.matlab")
}
if(!require("readxl")){
  install.packages("readxl")
}

if(!require("dplyr")){
  install.packages("dplyr")
}
if(!require("readxl")){
  install.packages("readxl")
}

if(!require("ggplot2")){
  install.packages("ggplot2")
}

if(!require("caret")){
  install.packages("caret")
}

if(!require("glmnet")){
  install.packages("glmnet")
}

if(!require("WeightedROC")){
  install.packages("WeightedROC")
}

library(R.matlab)
library(readxl)
library(dplyr)
library(EBImage)
library(ggplot2)
library(caret)
library(glmnet)
library(WeightedROC)
library(randomForest)
library(ROSE)
# library(tidymodels)
# library(doParallel)

Step 0 set work directories

set.seed(2020)
#setwd("C:/Users/Bee/Desktop/2020 FALL/github/Fall2020-Project3-group_2/doc")

Provide directories for training images. Training images and Training fiducial points will be in different subfolders.

train_dir <- "../data/train_set/" # This will be modified for different data sets.
train_image_dir <- paste(train_dir, "images/", sep="")
train_pt_dir <- paste(train_dir,  "points/", sep="")
train_label_path <- paste(train_dir, "label.csv", sep="") 

Step 1: set up controls for evaluation experiments.

In this chunk, we have a set of controls for the evaluation experiments.

• (T/F) cross-validation on the training set
• (T/F) reweighting the samples for training set
• (number) K, the number of CV folds
• (T/F) process features for training set
• (T/F) run evaluation on an independent test set
• (T/F) process features for test set

 run.cv <- TRUE # run cross-validation on the training set
 sample.reweight <- TRUE # run sample reweighting in model training
 K <- 5  # number of CV folds
 run.feature.train <- TRUE # process features for training set
 run.test <- TRUE # run evaluation on an independent test set
 run.feature.test <- TRUE # process features for test set

Using cross-validation or independent test set evaluation, we compare the performance of models with different specifications. In this Starter Code, we tune parameter lambda (the amount of shrinkage) for logistic regression with LASSO penalty.

ntree = c(60,80,100)
model_rf = paste("Random Forest with number of trees =", ntree)

Step 2: import data and train-test split

#train-test split
info <- read.csv(train_label_path)
n <- nrow(info)
n_train <- round(n*(4/5), 0)
set.seed(0)
train_idx <- sample(info$Index, n_train, replace = F)
test_idx <- setdiff(info$Index, train_idx)

If you choose to extract features from images, such as using Gabor filter, R memory will exhaust all images are read together. The solution is to repeat reading a smaller batch(e.g 100) and process them.

n_files <- length(list.files(train_image_dir))

# image_list <- list()
# for(i in 1:100){
#    image_list[[i]] <- readImage(paste0(train_image_dir, sprintf("%04d", i), ".jpg"))
# }

Fiducial points are stored in matlab format. In this step, we read them and store them in a list.

#function to read fiducial points
#input: index
#output: matrix of fiducial points corresponding to the index
readMat.matrix <- function(index){
     return(round(readMat(paste0(train_pt_dir, sprintf("%04d", index), ".mat"))[[1]],0))
}

#load fiducial points
fiducial_pt_list <- lapply(1:n_files, readMat.matrix)
save(fiducial_pt_list, file="../output/fiducial_pt_list.RData")

Step 3: construct features and responses

• The follow plots show how pairwise distance between fiducial points can work as feature for facial emotion recognition.

  • In the first column, 78 fiducials points of each emotion are marked in order.
  • In the second column distributions of vertical distance between right pupil(1) and right brow peak(21) are shown in histograms. For example, the distance of an angry face tends to be shorter than that of a surprised face.
  • The third column is the distributions of vertical distances between right mouth corner(50) and the midpoint of the upper lip(52). For example, the distance of an happy face tends to be shorter than that of a sad face.

Figure1

feature.R should be the wrapper for all your feature engineering functions and options. The function feature( ) should have options that correspond to different scenarios for your project and produces an R object that contains features and responses that are required by all the models you are going to evaluate later.

• feature.R
• Input: list of images or fiducial point
• Output: an RData file that contains extracted features and corresponding responses

source("../lib/feature.R")
tm_feature_train <- NA
if(run.feature.train){
  tm_feature_train <- system.time(dat_train <- feature(fiducial_pt_list, train_idx))
  save(dat_train, file="../output/feature_train.RData")
}else{
  load(file="../output/feature_train.RData")
}

tm_feature_test <- NA
if(run.feature.test){
  tm_feature_test <- system.time(dat_test <- feature(fiducial_pt_list, test_idx))
  save(dat_test, file="../output/feature_test.RData")
}else{
  load(file="../output/feature_test.RData")
}

# dim(dat_train)
# ##[1] 2400 6007
# dim(dat_test)
# ##[1]  600 6007

Step 4: Train a classification model with training features and responses

Call the train model and test model from library.

train.R and test.R should be wrappers for all your model training steps and your classification/prediction steps.

• train.R
  • Input: a data frame containing features and labels and a parameter list.
  • Output:a trained model
• test.R
  • Input: the fitted classification model using training data and processed features from testing images
  • Input: an R object that contains a trained classifier.
  • Output: training model specification
• In this Starter Code, we use logistic regression with LASSO penalty to do classification.

source("../lib/train_rf.R")
source("../lib/test_rf.R")
source("../lib/cross_validation_rf.R")
source("../lib/cross_validation_rf_weighted.R")

Model selection with cross-validation without weighting

res_cv_rf <- as.data.frame(res_cv_rf)
colnames(res_cv_rf) <- c("mean_error", "sd_error")
res_cv_rf$ntree = as.integer(ntree)
res_cv_rf

Model selection with cross-validation with weighting

res_cv_rf_w <- as.data.frame(res_cv_rf_w)
colnames(res_cv_rf_w) <- c("mean_error", "sd_error")
res_cv_rf_w$ntree = as.integer(ntree)
res_cv_rf_w

#
if(run.cv){
  res_cv_total <- rbind(res_cv_rf,res_cv_rf_w)
  ntree_best <- res_cv_total$ntree[which.min(res_cv_total[,1])]
}
save(ntree_best,file = "../output/ntree_best_rf.Rdata")

##Training
tm_train=NA
tm_train <- system.time(fit_train_rf <- train_rf(dat_train, ntree_best))
save(fit_train_rf, file="../output/fit_train_rf.RData")

##Testing
tm_test=NA
if(run.test){
  load(file="../output/fit_train_rf.RData")
  tm_test <- system.time(pred_rf <- predict(fit_train_rf,dat_test))
}

##evaluation
test_label <- dat_test$label
accu <- mean(test_label == pred_rf)
tpr.fpr <- WeightedROC(as.numeric(pred_rf), test_label)
auc <- WeightedAUC(tpr.fpr)

cat("The accuracy of model:", model_rf[which.min(res_cv_rf$mean_error)], "is", accu*100, "%.\n")

## The accuracy of model: Random Forest with number of trees = 100 is 81.66667 %.

cat("The AUC of model:", model_rf[which.min(res_cv_rf$mean_error)], "is", auc, ".\n")

## The AUC of model: Random Forest with number of trees = 100 is 0.5370982 .

Summarize Running Time

Prediction performance matters, so does the running times for constructing features and for training the model, especially when the computation resource is limited.

cat("Time for constructing training features=", tm_feature_train[1], "s \n")

## Time for constructing training features= 3.5 s

cat("Time for constructing testing features=", tm_feature_test[1], "s \n")

## Time for constructing testing features= 0.37 s

cat("Time for training model=", tm_train[1], "s \n") 

## Time for training model= 180.15 s

cat("Time for testing model=", tm_test[1], "s \n")

## Time for testing model= 1.16 s

###Reference - Du, S., Tao, Y., & Martinez, A. M. (2014). Compound facial expressions of emotion. Proceedings of the National Academy of Sciences, 111(15), E1454-E1462.